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SANTA CLARA, Calif. — From the moment the San Francisco 49ers’ 2025 season ended, it was fair to wonder whether quarterback Mac Jones would remain with the team in 2026.
Jones started eight games in place of injured starter Brock Purdy, leading the Niners to a 5-3 record and keeping them afloat in the NFC playoff chase. It was a win-win scenario that also allowed Jones to get his career headed in the right direction. At their end-of-season meeting, the Niners and Jones had honest discussions about his future and any potential trades to a team in need of a starting signal-caller. Jones was told that while a deal was possible, it would take a substantial offer to pry him away from the Bay Area.
During draft weekend, coach Kyle Shanahan hinted that it would have taken at least a first-round pick for the Niners to sacrifice their quarterback depth.
"It really surprised me that no one came and offered something," Shanahan said after the first round of the draft. "And his value has probably already passed anyway."
Now, with the 49ers' offseason program complete, it's likely that Jones will play out the final season of the two-year deal he signed in San Francisco.
The Niners and Jones recently revised his contract, adding a $300,000 roster bonus that will allow Jones to make $3.55 million in 2026 with another $2.25 million available in incentives before he hits unrestricted free agency next offseason. Asked recently about the adjustment to his contract, Jones declined to get into details, noting only that it "was something to do with last year," but that he's "really grateful" for it.
One possibility for the tweak was an incentive in his contract that would have allowed Jones to earn an additional $550,000 had he both played 50% of the regular-season snaps and the Niners earned a postseason bid. While the 49ers made the playoffs, Jones played 48.6% of the offensive snaps, coming up just shy of qualifying.
Regardless of any of that, Jones made it clear that he's happy to remain in San Francisco after previous turbulent seasons in New England and Jacksonville.
"I think there was some stuff out there and it was made very clear to me that I was going to be here from this organization," Jones said. "I'm fired up about it and I kind of knew that was the situation early in the offseason. … Obviously you want to have a chance to start, but I also love it here and I'm not really in the business of leaving good people so I'm not mad about it at all."
Multiple things worked against a possible deal for Jones. For one, many of the teams in need of help at the position such as the Miami Dolphins, the New York Jets and Arizona Cardinals are in rebuilding mode and reluctant to trade away valuable draft capital as they look to the future.
Then, for a team such as the Minnesota Vikings, which was believed to be Jones' preferred destination outside of San Francisco, it was easier and cheaper to sign Kyler Murray to a league-minimum deal because of offset language in his contract, than it was to deal a pick and then potentially sign Jones to a lucrative extension.
There is, of course, still a path to Jones getting another starting job in the near future.
For Jones, the chance to string two good seasons together — something he hasn't done as a pro yet — would only bolster his position before hitting free agency in 2027. What he did in 2025 was a step in the right direction.
Arriving in San Francisco after posting a combined QBR of just 37.6 over the previous three seasons (2022-23 in New England and 2024 in Jacksonville), Jones acknowledged that his fledgling career was trending in the wrong direction.
When he hit free agency last offseason, Jones targeted San Francisco as the place that could revive his career. He had seen Sam Darnold have success as another former top pick who stopped over with Shanahan and the Niners and believed he could perform a similar career surgery.
Unlike Darnold, however, Jones signed a two-year deal with the Niners. It was an unusual step and one that prevented Jones from cashing in as a free agent this year.
But Jones doesn't quite see that decision as a bad thing.
"I think it's hard because what if it went the other way?" Jones said. "What if I was on a one-year deal and played like crap then I'm on the street. I'll take any years you can get in the league. Just being on a team is a blessing for me and obviously I have a higher ceiling than just that, but that's the basis. So, you want to make sure you're good to go so I'm not stressing about it. I think it's all good …
"The one-year or two-year thing is definitely a legit question, but it'll all work out how it's supposed to."
For now, Jones is searching for ways to build on the best season he's had since his rookie year in New England in 2021. In eight games last season, Jones threw for 13 touchdowns with six interceptions while averaging 268.9 passing yards per game. His 62.3 QBR was 10th in the NFL.
Throughout, Jones attributed his improved play to strong coaching from the likes of Shanahan, offensive coordinator Klay Kubiak and quarterbacks coach Mick Lombardi as well as support from Purdy and other quarterbacks. He also noted the importance of rebuilding his confidence after some disappointing seasons.
"I think he came in here with maybe that mindset, but with any new player you get on a new team, you try and just treat him with a blank slate," Lombardi said. "It's like, I don't really care what happened last year. That was really fun and awesome, but this is 2026, not 2025. We have a short-term memory in terms of success and failures. I'm going to try and build and focus on what we need to improve on this year, as opposed to focus on what happened last year."
Jones didn't get to do much on-field work during organized team activities because of soreness in his right (throwing) shoulder but said it's nothing serious and he should be ready for training camp in July.
He also points out that with Kubiak and Shanahan in place; this will be the first time since he entered the NFL that he will be in the same system with the same coordinator two years in a row.
At the end of last season, Jones told ESPN he felt like he "got the train back on the tracks." The mission now is finding a way to keep it from derailing. Jones jokes that he's not an engineer, but he has given plenty of thought to what he can do to ensure he stays on course.
"I know that if I go out there on Sunday and have the right mindset that I can play really good football and I proved that last year," Jones said. "But the challenge is to do it again this year and really not compare the two. Every season is different and I've learned that probably better than anybody … I feel like it's time to stack some good years here."
